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mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

moore_darkside

A publicly accessible location for access to data and analysis relating to the Moore Foundation project “Life on the Dark Side”: Complex trophic interactions of marine microbial eukaryotes.

orchard

:seedling: :clipboard: :arrow_right: :8ball: :arrow_right: :palm_tree: :evergreen_tree: :deciduous_tree: - A quick phylogenetic tree building pipeline!

orcharddb

:apple: :deciduous_tree: A script to create and populate a local database of amino acid sequences combined with taxonomic information, the AA gene predictions can be retrieved from a variety of genome-portals and then used with the Orchard tree building pipeline.

orthagogue

Automatically exported from code.google.com/p/orthagogue

orthomcl-pipeline

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/

orthomcl_tools

A couple of tools I find indispensable for post orthomcl down-stream analysis.

paramecium

Scripts and data file for An RNAi-dependent punishment for algal elimination in a phototrophic endosymbiosis.

phylogenomic-analysis

Useful scripts for conducting phylogenomic analyses.

planktoscope

Low-cost fluidic microscope for citizen science

pr2-curation

PR2 curation: a shiny app version of the EukRef data curation pipeline

predict_secretome

Secretome prediction pipeline

protists.co.uk

random_scripts

A collection of random scripts I have made over the years, barely any documentation though. Enjoy, be careful!

reddit-perl-api

A simple Perl API to query Reddit

refgen

A time-saving tool to change the 'defline' of FASTA files for a range of phylogenetic programs e.g. ClustalX, MrBayes, PhyML

sagawe

:white_circle: :arrow_right: :mag: :information_source: A suggested workflow, and accompanying scripts, to assemble Single Amplified Genomes (SAGs) from MDA derived Hi/MiSeq (Overlapped) Paired-End Illumina Libraries.

sequenceserver

Intuitive local web frontend for sequence BLAST (www search form)

tadpole-doctor.co.uk

taxa_autocorrect

A tool to 'automagically' italicise taxon names, compiled from 839 taxa sampled from NCBI, DOE JGI and BROAD. Currently MS Word only

taxdump_edit

:seedling: :arrow_right: :deciduous_tree: Add new taxa or taxonomic groups to the NCBI Taxdump files

transcriptomics_2017

treenamer

tutorials

A few simple tutorials for our lab group sessions.

ukraine

Help Ukraine - add ribbon with Ukraine flag into the website you manage, show the anti-war message to Russian users, or block them from your service.

upsetr

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

web

Web content for Meren Lab